Comparative analysis of microRNA expression in serum and plasma in patients screened for BRCA1 or BRCA2 mutations

MicroRNA-based biomarkers hold promise for precision oncology, but standardization and pre-analytical variability remain barriers to clinical use. We performed a technical study to assess how the type of biological material (plasma, serum) and quantification (miRNA-seq, RT-qPCR) method affect microRNA (miRNA) levels. Samples from 202 women – 154 carriers of BRCA1/2 pathogenic variants, from three centers were collected. MiRNAs were quantified using miRNA sequencing (miRNA-seq), a quantitative PCR (qPCR) panel of 182 miRNAs (Qiagen) or targeted qPCR of 13 miRNA associated with BRCA mutations or ovarian cancer. Differential expression and linear regression analyses were used to assess methods concordance and biological material-related differences. Differences of individual miRNA levels between serum and plasma were more pronounced in sequencing than in qPCR. miR-193a-3p, miR-197-3p, miR-877-5p and miR-2110 were detected in significantly higher amounts in serum, while miR-28-5p in plasma, by both sequencing and qPCR. Measurements done by sequencing and qPCR correlated positively and significantly for ~ 75% of investigated miRNA. Finally, strong inter-assay correlation of established qPCR hemolysis marker (based on miR-451a and miR-23a-3p) provided evidence that it can be used also in sequencing data. Differences in absolute and relative miRNA levels in serum and plasma necessitate material-specific test calibration and may impact selection of best miRNA biomarkers for specific scenarios. Concordance in expression levels quantified by miRNA-seq and qPCR is generally good for high-expression miRNAs in both serum and plasma, but a conversion of multi-miRNA tests from serum to plasma is unfeasible without experimental calibration.